2023 CODEX HCC article Segmentation output raw datasets

Published: 5 February 2024| Version 1 | DOI: 10.17632/6w2k42kytt.1
Xinyao Qiu


This file contains the Segmentation results by StarDist in Qupath. The analysis method can be found in the manuscript. Each TMA contains multiple regions in it. Each region represents a tissue spot in TMA. The clinical information was in HCC401_new.Rdata. Each row in the seg-file represents the information of a single cell, containing the marker intensity, the x and y coordinates, and some other segmentation-related information. HCC401_new.Rdata and Qupath cell segmentation ouptut.zip can serve as the input of Part 1 "discovery cohort pre-processing and cell type phenotype definition" in https://github.com/sanrishiguang/ChenleiLab_CODEX_HCC. And the output file of Part 1 with defined cell type/phenotype information was testing_allReg_seurat_._analysis_20220315_AllSubtypes_withoutartifact.csv. HCC401_new.Rdata and the output file of Part 1 are provided in https://data.mendeley.com/datasets/km2df7y256/1.


Steps to reproduce

The analysis method can be found in the manuscript.


Fudan University Shanghai Cancer Center, Eastern Hepatobiliary Surgery Hospital


Big Data, Data Array


National Natural Science Foundation of China

81830054, 81902412, 91859205, 82002921